Biomark HD

Production-scale throughput with exquisite single-cell sensitivity and consistent results

High-Definition Biology

No more compromising for quality. With the Biomark™ HD system, you get reliable production-scale throughput and exquisite single-cell sensitivity, with a wide variety of sample types and chemistry choices to accommodate the most genomic applications. Now you can run entire projects from research to validation to routine screening on a single system with the flexibility you want and the consistency you need. Anything else we can help with?


Design experiments to match your needs across the widest range of genomic applications.


Detect unique molecular signatures in individual cells and rare cell populations.


Accelerate discovery with a higher throughput and automated workflow.


Conserve precious samples—and funding—with lower reagent use and nanoliter reactions.


Fluidigm’s revolutionary integrated fluidic circuits (IFCs) empower life science research by automating PCR reactions in nanoliter volumes. This means using less sample and reagent, and a single microfluidic device, to achieve the high-quality, consistent results your work depends on. The Biomark HD system runs IFCs in either real-time or end-point read modes, bringing flexible, efficient and economical PCR solutions to a range of applications.


  1. Prime
  2. Transfer
  3. Load
  4. Run
  5. Analyze


Prime the Dynamic Array IFC to prepare it for sample transfer.


Pipet samples and primer-probe sets into the designated inlets on the IFC.


Load the IFC on the controller, which prepares the reactions.


Place the IFC into Biomark for thermal cycling and end-point or real-time fluorescence detection.


View and analyze color-coded expression heat maps, allele maps and cluster plots for single or multiple runs with our analysis software.


Biomark & EP1 Support

Explore tutorials and publications, browse frequently asked questions, download technical documents, review training programs and service plans and locate the right IFCs, kits and reagents for your research. Still need help? Reach out to one of our support specialists here


IFCs, Assays and Reagents

Digital Array IFCs

Ensure a precise determination of copy number variation with this innovative IFC designed specifically for digital PCR experiments.

Dynamic Array IFCs

Experience a new level of efficiency and throughput for gene expression and genotyping applications with the Fluidigm Dynamic Array™ IFCs used together with the Juno and Biomark HD systems.

SNP Type Assays

SNP Type™ assays provide a high-throughput, low-cost single-nucleotide polymorphism (SNP) genotyping solution enabling rapid assay design for efficient variant screening. The assays are based on allele-specific PCR SNP detection chemistry and are available for use with Fluidigm IFC technology on Biomark HD, EP1™ and Juno™ systems.

D3 Assay Design

Simplify your assay design with our D3™ tool, which enables you to easily define parameters for customized targeted DNA sequencing, gene expression and genotyping. For species not supported online, support is available from the D3 expert design team.

Delta Gene Assays

Realize the full potential of your Biomark™ HD system with minimal setup time and validated protocols that yield quality gene expression results. Just specify your genes of interest and target species to order our exclusive, high-quality, economical and MIQE-compliant Delta Gene™ assays (formerly DELTAgene). Designed specifically for use with Dynamic Array IFCs.

  1. Digital Array IFCs
  2. Dynamic Array IFCs
  3. SNP Type Assays
  4. D3 Assay Design
  5. Delta Gene Assays

Related Systems

IFC Controllers

IFC Controllers Benefit from fewer steps and automated setup of our Dynamic Array™ and Digital Array™ IFCs with Fluidigm’s highly efficient IFC controllers.
  1. IFC Controllers


Biomark Pathogen Detection Software v2.1.1

Software that analyzes qPCR Ct data from Biomark HD to detect and identify mutations. For installation and instructions please reference the Biomark Pathogen Detection Software Quick Reference Guide- (FLDM-00557).)

Biomark & EP1 Software

The latest software for the Biomark™ HD, Biomark and EP1™ systems. Package includes software for data collection, real-time PCR analysis, genotyping, digital PCR and melting curve analysis. To install, follow the instructions in the Updating the Biomark/EP1 Software Quick Reference (PN 101-6793). 

IFC Controllers Software (HX, MX, RX, and WX)

The latest software for IFC Controllers HX, MX, RX and WX. To install, follow the instructions in the Update Software and Scripts section of the relevant IFC Controller User Guide (HX/MX, PN 68000112; RX, PN 100-3385; WX, PN 100-2297). 

Singular Analysis Toolset Software

An innovative, open-source solution for analyzing and visualizing data, the Singular™ Analysis Toolset offers powerful methods for identifying gene expression and mutation patterns at the single-cell level. Designed for use with Biomarkand C1 systems.

CopyCount-CNV Software

The cloud-based software analyzes raw fluorescence qPCR data from Biomark™ HD to determine absolute quantification and provide DNA copy number results. Applications include transgene copy number, event-sorting data analysis, and seed zygosity determination.

Each license supports one year of use from the date of activation and may be ordered through your Fluidigm account representative.

GO Immuno-Oncology Workbench

GO Immuno-Oncology Workbench is designed to further analyze primary data obtained with the Advanta™ IO Gene Expression Assay. GO Immuno-Oncology Workbench enables users to analyze large cohorts, discover population-level trends and accelerate checkpoint inhibitor research. It is designed by GenomOncology, a leader in the field of cancer molecular pathology analysis.

Each license supports one year of use from the date of activation and may be ordered through your Fluidigm account representative. 

  1. Biomark Pathogen Detection Software v2.1.1
  2. Biomark & EP1 Software
  3. IFC Controllers Software (HX, MX, RX, and WX)
  4. Singular Analysis Toolset Software
  5. CopyCount-CNV Software
  6. GO Immuno-Oncology Workbench


Instrument (Part Number BMKHD-BMKHD)

Depth 75 cm (29.5 in)
Width 75 cm (29.5 in)
Height 100 cm (39.4 in)
Weight 140 kg (308 lb)
Thermal Control Peltier-based, 4–99 ºC
Heating ramp rate Up to 5.5 ºC/sec
Cooling ramp rate Up to 5.5 ºC/sec
Detection CCD camera; 9M pixel, 12 μm x 12 μm pixel size
Fluorescence excitation 475 nm, 530 nm, 575 nm
Fluorescence emission 525 nm, 570 nm, 630 nm
Power requirements 100–230 VAC, 50/60 Hz, 300 W
Fluidigm provides a region-specific power cord for the Biomark HD system.
Instrument Control Computer
Computation Intel® Core™ i3-2120, 3.30 GHz
Memory 2GB
Storage 500 GB HDD
Ports 4 USB
1GB/sec Ethernet
Operating System Microsoft® Windows® 10 IoT Enterprise 2016 LTSB (32 bit)
Monitor LCD flat panel
Accessories Keyboard and mouse

Work Environment (indoor use only)

Temperature 15–30 ºC (59–86 ºF)
Humidity 20%–80% relative humidity, non-condensing
Altitude Not to exceed 2,000 m (6,560 ft) above sea level

Supported IFCs

Gene expression 48.48 Dynamic Array™ IFC
96.96 Dynamic Array IFC
192.24 Gene Expression IFC
Flex Six™ Gene Expression IFC
Genotyping 48.48 Dynamic Array IFC
96.96 Dynamic Array IFC
192.24 Genotyping IFC
Flex Six Genotyping IFC
Digital PCR qdPCR 37K™ IFC
48.770 Digital Array™ IFC
12.765 Digital Array IFC


Data Collection Biomark HD Data Collection software
Analysis Real-Time PCR Analysis software
SNP Genotyping Analysis software
Digital PCR Analysis software
Melt Curve Analysis software